MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b3115 b1849 b2296 b2926 b0160 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b2975 b3603 b0529 b2492 b0904 b3035 b1380 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.329593 (mmol/gDw/h)
  Minimum Production Rate : 0.518374 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.854518
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.189669
  EX_pi_e : 1.873050
  EX_so4_e : 0.082998
  EX_k_e : 0.064334
  EX_fe2_e : 0.005294
  EX_mg2_e : 0.002859
  EX_ca2_e : 0.001716
  EX_cl_e : 0.001716
  EX_cu2_e : 0.000234
  EX_mn2_e : 0.000228
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_h2o_e : 53.113092
  EX_co2_e : 33.001905
  EX_h_e : 6.394095
  EX_ac_e : 1.290693
  Auxiliary production reaction : 0.518374
  EX_hxan_e : 0.000369
  DM_5drib_c : 0.000221
  DM_4crsol_c : 0.000073

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

---

Last updated: 21-Sep-2023
Contact